Stevie Crawford netted their first SPL goal since December 10 from the penalty spot late in the first half, after Simon Ford had been sent off for felling Adam Hammill as the last defender.
Steven Naismith had an early chance for Killie, but Dorus De Vries cut down the angle and blocked his shot well. But Dunfermline did not heed the warning.
A minute later, they failed to deal with an up-and-under from Rocco Quinn and the ball broke kindly for Naismith, who scored with a low shot.
The Pars hit back but found Alan Combe in inspired form. He leapt to his left to tip a Hammill shot past his post and then came out bravely to block Stephen Simmons.
But a mistake by Ford cost Kilmarnock dearly in the final minute of the half. He was caught in possession 30 yards from his own goal and then chased back to bring Hammill down in the area.
Referee Mr Somers showed him the red card for being the last defender and Crawford stepped up to send Combe the wrong way with the spot-kick. It was Dunfermline's first league goal in 854 minutes of football.
Combe did well again to clutch a Simmons' header underneath his crossbar early in the second half as Dunfermline tried to cash in on their numerical advantage.
Scott Wilson then side-footed yards wide from ten yards after a Crawford cutback.
But a mistake by Dunfermline defender Wilson with 15 minutes left let in Colin Nish, but he shot straight at De Vries.